The Spider is a bit tricky. I mean it´s freaking fast. But there is still an easy way to kill it silently. Simply take a lantern (there are many of those in the near of big facilities) and throw it at the creature. It burns until almost a quarter of its health is gone. Just repeat it a few times and you got it! Easy right?
The Butcher is an easy one. You can simply pick up an axe or a hammer, and hit him with it. Normaly you should be able to hit him 3 times with the axe before your stamina has ran out. Be sure you are close to an exit so you can run out after you hit him!
Yeah, the youngest of all bosses. The Assassin. But he´s still as easy as the others. It´s the same as with the spider. Pick up a lantern, throw it at him and wait until he stops burning. Then repeat it!